The APD refund is simply a tax refund. It would be no different if the passenger held a fully flexible WT+ ticket and changed it voluntarily to WT. He should receive the tax refund having nothing to do with either EC 261/2004 or BA's COC.

As to the YQ, it is worth making a claim for 75% of it. I don't know that pursuing MCOL over it is worth doing unless the passenger is prepared to follow through to a contested resolution. This is not about the small sum, but about lines in the sand BA is likely to draw.

For what it is worth, the entire YQ concept should have been abolished long ago and the fare equal to the amount required to be paid in order to board the flight (+ taxes).

Expedia did a disservice to OP. I fully appreciate that this was a consolidator ticket and thus the segment fare is not 50% of the ticket price. Rather the ticket is simply the ticket. But, the fees & taxes are applied to all tickets and those could easily have been broken down for OP.